Actually, it is possible to remove the USB 3.0 hub. It requires a bit of skill with a soldering iron and SMT rework gear, but if you have the tech capabilities, the procedure is as follows (obviously, this will void any warranty; do it at your own risk, etc.). We have done this here and have verified using the USB 3.0 controller in device mode:

To Convert the TWR-LS1021A board to USB Device mode:

1) Remove the LS1021A Heatsink Clip (but not the heatsink)

2) Remove U29 (Top Of Board)

3) Remove U41 (Bottom Of Board)

4) Cut the 2 traces below C101 & C102 (to remove the stubs)

5) Cut the 2 traces to the right of C127 & C128 (to remove the stubs)

6) Prepare a USB3 cable with a Type A connector (you can cut the Type B connector off of a standard A->B cable)

7) Solder the TX pair conductors of the cable (e.g. TX from host) to the bottom pads of C101 and C1028) Solder the RX pair conductors of the cable (e.g. RX to host) to the bottom pads of C127 and C128

9) Solder the DP wire to pad 53 for U2910) Solder the DN wire to pad 54 for U29

11) Solder the VBUS wire to Pin1 of L31 (on the bottom of the board)

12) Solder the GND wire to the ground pad under U29

13) Wedge the cable with exposed shield between the shield cans of the Ethernet connectors to allow the cable to be mostly shielded

Now you can rebuild linux with gadget support and the DWC3 USB Controller in gadget mode. If you have a gadget driver loaded, the USB controller will connect to the host in device mode.